AMBER Archive (2007)

Subject: AMBER: Applying bugfixes in Amber

From: Lili Peng (lpeng_at_ucsd.edu)
Date: Thu Oct 04 2007 - 16:28:29 CDT

Hi all,

I'm trying to apply bugfix.12 (
http://amber.scripps.edu/bugfixes/9.0/bugfix.12) in using antechamber. I'm
not used to Linux commands, and I'm not sure what to enter when I reach
"File to patch". Below is a list of my commands:

which setenv
setenv AMBERHOME /usr/local/apps/amber9
echo $AMBERHOME
patch -p0 -N -r patch_rejects < bugfix.12

After I get this output below, the prompt "File to patch" comes up, and I
just don't know what to do so I pressed enter. I guess that was a dumb move
to do, since it didn't really do anything. Can someone please advise me in
what steps I should take?

Thanks,
Lili

"********>Bugfix 12:

Author: Scott Brozell
Date: 08/17/06

Programs: Antechamber

Description: Files of type prepi or prepc with a length greater than 139
             lines cause antechamber programs to fail. The -o output
             file contains garbage. The standard output usually contains:
Info: the atom number exceeds the MAXATOM, reallocate memory automatically
 Unrecognized atomic name , exit

Fix: apply the following patch to amber9/src/antechamber/prep.c *and* to
      amber9/src/antechamber/parmchk.c

------------------------------------------------------------------------------
*** prep.c 3 Apr 2006 23:34:26 -0000 9.0
--- prep.c 18 Aug 2006 05:02:19 -0000
***************
"
File to patch:

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu